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- EMDB-42348: Structural Basis of Human NOX5 Activation -

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Basic information

Entry
Database: EMDB / ID: EMD-42348
TitleStructural Basis of Human NOX5 Activation
Map data
Sample
  • Complex: NADPH oxidase 5
    • Protein or peptide: NADPH oxidase 5 (NOX5)
Keywordsenzyme / oxidase / activation mechanism / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.99 Å
AuthorsCui C / Jiang M / Sun J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM141357 United States
CitationJournal: To Be Published
Title: Structural Basis of Human NOX5 Activation
Authors: Cui C / Jiang M / Sun J
History
DepositionOct 12, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42348.png

Downloads & links

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Map

FileDownload / File: emd_42348.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 240 pix.
= 311.28 Å		1.3 Å/pix.
x 240 pix.
= 311.28 Å		1.3 Å/pix.
x 240 pix.
= 311.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.297 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-3.8598437 - 6.8588433
Average (Standard dev.)0.003203951 (±0.08615837)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 311.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_42348_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_42348_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NADPH oxidase 5

EntireName: NADPH oxidase 5
Components
  • Complex: NADPH oxidase 5
    • Protein or peptide: NADPH oxidase 5 (NOX5)

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Supramolecule #1: NADPH oxidase 5

SupramoleculeName: NADPH oxidase 5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: NADPH oxidase 5 (NOX5)

MacromoleculeName: NADPH oxidase 5 (NOX5) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MSAEEDARWL RWVTQQFKTI AGEDGEISLQ EFKAALHVKE SFFAERFFAL FDSDRSGTIT LQELQEALTL LIHGSPMDKL KFLFQVYDID GSGSIDPDEL RTVLQSCLRE SAISLPDEKL DQLTLALFES ADADGNGAIT FEELRDELQR FPGVMENLTI SAAHWLTAPA ...String:
MSAEEDARWL RWVTQQFKTI AGEDGEISLQ EFKAALHVKE SFFAERFFAL FDSDRSGTIT LQELQEALTL LIHGSPMDKL KFLFQVYDID GSGSIDPDEL RTVLQSCLRE SAISLPDEKL DQLTLALFES ADADGNGAIT FEELRDELQR FPGVMENLTI SAAHWLTAPA PRPRPRRPRQ LTRAYWHNHR SQLFCLATYA GLHVLLFGLA ASAHRDLGAS VMVAKGCGQC LNFDCSFIAV LMLRRCLTWL RATWLAQVLP LDQNIQFHQL MGYVVVGLSL VHTVAHTVNF VLQAQAEASP FQFWELLLTT RPGIGWVHGS ASPTGVALLL LLLLMFICSS SCIRRSGHFE VFYWTHLSYL LVWLLLIFHG PNFWKWLLVP GILFFLEKAI GLAVSRMAAV CIMEVNLLPS KVTHLLIKRP PFFHYRPGDY LYLNIPTIAR YEWHPFTISS APEQKDTIWL HIRSQGQWTN RLYESFKASD PLGRGSKRLS RSVTMRKSQR SSKGSEILLE KHKFCNIKCY IDGPYGTPTR RIFASEHAVL IGAGIGITPF ASILQSIMYR HQKRKHTCPS CQHSWIEGVQ DNMKLHKVDF IWINRDQRSF EWFVSLLTKL EMDQAEEAQY GRFLELHMYM TSALGKNDMK AIGLQMALDL LANKEKKDSI TGLQTRTQPG RPDWSKVFQK VAAEKKGKVQ VFFCGSPALA KVLKGHCEKF GFRFFQENF

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.99 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 220000

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